Is RDX p.Ser510= (c.1530C>T) pathogenic?

RDX p.Ser510= (c.1530C>T) is classified Conflicting classifications of pathogenicity in RDX (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2025-09-09). Rare (popmax 0.236%, eas); Associated with autosomal recessive nonsyndromic hearing loss 24.

What condition is associated with RDX p.Ser510= (c.1530C>T)?

RDX p.Ser510= (c.1530C>T) is associated with autosomal recessive nonsyndromic hearing loss 24 (ClinVar).

How common is RDX p.Ser510= (c.1530C>T) in the general population?

RDX p.Ser510= (c.1530C>T) is rare (popmax 0.236%, eas) (gnomAD).

RDX p.Ser510=

c.1530C>T · rs192239366 · VCV302342

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.236%, eas)

Conditions

autosomal recessive nonsyndromic hearing loss 24

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.17	GERP -5, phastCons 0.15
Overall
CADD	9.575	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.236% East Asian · 106/44,878 alleles

Filtering AF 0.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.186%

Overall 0.00849% 137/1,613,840 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.236%	423
Remaining individualsnot grpmax-eligible	0.0176%	5,681
Admixed American	0.00833%	12,002
South Asian	0.00659%	15,177
African / African-American	0.00133%	74,932
European (non-Finnish)	0.000678%	147,497

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: RDX
Protein: p.Ser510=
Coding: c.1530C>T
MANE Select: NM_002906
dbSNP: rs192239366
Type: single nucleotide variant
Location: chr11:110233294 (GRCh38)
Gene constraint: LOEUF 0.542 · pLI 0.66 (gnomAD)
Structure: AlphaFold pLDDT 86.98 · 2 PDB
Residue 510: the 'disordered' region

Full RDX gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autosomal recessive nonsyndromic hearing loss 24 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

RDX c.*156A>G Uncertain significance ★★ same condition
RDX c.*2006A>G Uncertain significance ★★ same condition
RDX c.*79A>C Uncertain significance ★★ same condition
RDX p.Arg350His Uncertain significance ★★ ⚠ same condition
RDX p.Asn502Asp Uncertain significance ★★ ⚠ same condition
RDX p.Lys526Arg Uncertain significance ★★ ⚠ same condition
RDX p.Pro471Ala Uncertain significance ★★ ⚠ same condition
RDX p.Ser501Pro Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/rdx-p-ser510 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown